Starting phenix.real_space_refine on Thu Aug 6 15:27:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cli_16713/08_2026/8cli_16713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cli_16713/08_2026/8cli_16713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cli_16713/08_2026/8cli_16713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cli_16713/08_2026/8cli_16713.map" model { file = "/net/cci-nas-00/data/ceres_data/8cli_16713/08_2026/8cli_16713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cli_16713/08_2026/8cli_16713.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8cli_16713/08_2026/8cli_16713.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cli_16713/08_2026/8cli_16713.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 70 5.49 5 S 93 5.16 5 C 9953 2.51 5 N 2816 2.21 5 O 3021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15955 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4421 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 522} Chain breaks: 4 Chain: "B" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5496 Classifications: {'peptide': 689} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 653} Chain breaks: 2 Chain: "C" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4601 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 534} Chain breaks: 1 Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 721 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "E" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 714 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9303 SG CYS B 747 88.806 71.398 116.033 1.00122.97 S ATOM 9323 SG CYS B 750 86.680 73.366 118.400 1.00130.50 S ATOM 9437 SG CYS B 764 87.358 69.709 119.224 1.00132.00 S ATOM 9642 SG CYS B 788 93.860 53.177 98.783 1.00 64.43 S ATOM 9853 SG CYS B 814 96.413 52.371 101.828 1.00 81.43 S ATOM 9877 SG CYS B 817 94.743 50.771 99.424 1.00 79.12 S Time building chain proxies: 3.41, per 1000 atoms: 0.21 Number of scatterers: 15955 At special positions: 0 Unit cell: (138.918, 99.462, 135.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 93 16.00 P 70 15.00 O 3021 8.00 N 2816 7.00 C 9953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 623.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" ND1 HIS B 768 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 750 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 747 " pdb="ZN ZN B 901 " - pdb=" SG CYS B 764 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 814 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 788 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 817 " Number of angles added : 3 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3412 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 22 sheets defined 31.1% alpha, 22.3% beta 35 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.690A pdb=" N GLU A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 205 through 219 removed outlier: 4.521A pdb=" N ILE A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 253 through 269 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 286 through 300 removed outlier: 4.163A pdb=" N ARG A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 431 through 435 removed outlier: 4.661A pdb=" N GLU A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 435' Processing helix chain 'A' and resid 437 through 456 Processing helix chain 'A' and resid 611 through 628 Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.582A pdb=" N ILE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 Processing helix chain 'A' and resid 700 through 715 Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.696A pdb=" N ALA B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 467 through 473 removed outlier: 3.829A pdb=" N VAL B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 527 Processing helix chain 'B' and resid 532 through 535 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.635A pdb=" N LEU B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 568 Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.708A pdb=" N TRP B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 696 Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'B' and resid 724 through 738 Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'C' and resid 300 through 322 Proline residue: C 306 - end of helix removed outlier: 3.742A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS C 312 " --> pdb=" O TRP C 308 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 341 through 346 Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.546A pdb=" N LEU C 519 " --> pdb=" O HIS C 515 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 522 " --> pdb=" O ALA C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 679 Processing helix chain 'C' and resid 740 through 744 removed outlier: 3.524A pdb=" N ASN C 743 " --> pdb=" O ASN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 749 Processing helix chain 'C' and resid 786 through 792 Processing helix chain 'C' and resid 808 through 811 Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 871 through 889 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 230 Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 275 Processing sheet with id=AA4, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AA5, first strand: chain 'A' and resid 582 through 583 Processing sheet with id=AA6, first strand: chain 'A' and resid 678 through 681 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 59 removed outlier: 7.482A pdb=" N ARG B 54 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR B 514 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE B 512 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR B 488 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B 482 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 490 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 480 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 492 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 72 removed outlier: 4.146A pdb=" N VAL B 103 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 169 removed outlier: 7.087A pdb=" N LEU B 191 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP B 207 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 193 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 257 removed outlier: 6.645A pdb=" N LEU B 279 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET B 251 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 277 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP B 253 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 275 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY B 255 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER B 273 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN B 291 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE B 300 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 323 removed outlier: 6.153A pdb=" N ILE B 340 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 381 removed outlier: 3.789A pdb=" N SER B 373 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 386 " --> pdb=" O HIS B 381 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER B 387 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE B 406 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 399 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 428 through 431 removed outlier: 3.637A pdb=" N SER B 428 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 447 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 761 through 763 Processing sheet with id=AB6, first strand: chain 'B' and resid 786 through 787 Processing sheet with id=AB7, first strand: chain 'C' and resid 337 through 339 removed outlier: 5.037A pdb=" N VAL C 535 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE C 459 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 443 " --> pdb=" O PHE C 459 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 461 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU C 438 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER C 419 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 358 through 362 removed outlier: 6.448A pdb=" N SER C 359 " --> pdb=" O PHE C 798 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP C 800 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN C 361 " --> pdb=" O ASP C 800 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 729 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 710 " --> pdb=" O GLY C 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 378 through 379 removed outlier: 3.927A pdb=" N SER C 378 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU C 860 " --> pdb=" O GLY C 856 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 856 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 470 through 475 removed outlier: 3.761A pdb=" N ASP C 472 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 513 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 498 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE C 511 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA C 500 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU C 509 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 539 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 557 through 562 removed outlier: 4.170A pdb=" N MET C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 607 " --> pdb=" O PHE C 582 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.654A pdb=" N ASN C 651 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 658 through 662 removed outlier: 4.057A pdb=" N GLU C 660 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 674 " --> pdb=" O GLY C 685 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY C 685 " --> pdb=" O GLN C 674 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 686 " --> pdb=" O THR C 701 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4907 1.34 - 1.46: 3603 1.46 - 1.58: 7683 1.58 - 1.70: 138 1.70 - 1.83: 137 Bond restraints: 16468 Sorted by residual: bond pdb=" C3' DT D 10 " pdb=" C2' DT D 10 " ideal model delta sigma weight residual 1.516 1.556 -0.040 8.00e-03 1.56e+04 2.50e+01 bond pdb=" C3' DT D 7 " pdb=" C2' DT D 7 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.29e+01 bond pdb=" C3' DC E 63 " pdb=" C2' DC E 63 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.88e+01 bond pdb=" C3' DC E 58 " pdb=" C2' DC E 58 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.75e+01 bond pdb=" C3' DT D 31 " pdb=" C2' DT D 31 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.54e+01 ... (remaining 16463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 21172 1.41 - 2.82: 1171 2.82 - 4.24: 199 4.24 - 5.65: 55 5.65 - 7.06: 9 Bond angle restraints: 22606 Sorted by residual: angle pdb=" O5' DG D 5 " pdb=" C5' DG D 5 " pdb=" C4' DG D 5 " ideal model delta sigma weight residual 109.40 116.07 -6.67 8.00e-01 1.56e+00 6.95e+01 angle pdb=" O5' DA D 4 " pdb=" C5' DA D 4 " pdb=" C4' DA D 4 " ideal model delta sigma weight residual 109.40 115.43 -6.03 8.00e-01 1.56e+00 5.67e+01 angle pdb=" O5' DG E 52 " pdb=" C5' DG E 52 " pdb=" C4' DG E 52 " ideal model delta sigma weight residual 109.40 114.77 -5.37 8.00e-01 1.56e+00 4.51e+01 angle pdb=" O4' DA D 4 " pdb=" C1' DA D 4 " pdb=" N9 DA D 4 " ideal model delta sigma weight residual 108.00 112.26 -4.26 7.00e-01 2.04e+00 3.70e+01 angle pdb=" O5' DA E 44 " pdb=" C5' DA E 44 " pdb=" C4' DA E 44 " ideal model delta sigma weight residual 109.40 114.18 -4.78 8.00e-01 1.56e+00 3.58e+01 ... (remaining 22601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.22: 9303 32.22 - 64.44: 410 64.44 - 96.66: 26 96.66 - 128.88: 0 128.88 - 161.10: 2 Dihedral angle restraints: 9741 sinusoidal: 4474 harmonic: 5267 Sorted by residual: dihedral pdb=" CA GLU B 68 " pdb=" C GLU B 68 " pdb=" N PRO B 69 " pdb=" CA PRO B 69 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ILE A 631 " pdb=" C ILE A 631 " pdb=" N GLU A 632 " pdb=" CA GLU A 632 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER B 85 " pdb=" C SER B 85 " pdb=" N ILE B 86 " pdb=" CA ILE B 86 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 9738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2176 0.079 - 0.158: 314 0.158 - 0.236: 16 0.236 - 0.315: 1 0.315 - 0.394: 1 Chirality restraints: 2508 Sorted by residual: chirality pdb=" C3' DG D 6 " pdb=" C4' DG D 6 " pdb=" O3' DG D 6 " pdb=" C2' DG D 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.34 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C1' DA D 18 " pdb=" O4' DA D 18 " pdb=" C2' DA D 18 " pdb=" N9 DA D 18 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C3' DT D 35 " pdb=" C4' DT D 35 " pdb=" O3' DT D 35 " pdb=" C2' DT D 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2505 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 796 " 0.303 9.50e-02 1.11e+02 1.37e-01 1.49e+01 pdb=" NE ARG B 796 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 796 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG B 796 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 796 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 186 " -0.295 9.50e-02 1.11e+02 1.33e-01 1.40e+01 pdb=" NE ARG A 186 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 186 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 186 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 186 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 841 " 0.289 9.50e-02 1.11e+02 1.31e-01 1.38e+01 pdb=" NE ARG C 841 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG C 841 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG C 841 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG C 841 " -0.000 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 72 2.56 - 3.14: 12588 3.14 - 3.73: 24998 3.73 - 4.31: 36290 4.31 - 4.90: 59180 Nonbonded interactions: 133128 Sorted by model distance: nonbonded pdb=" OD1 ASP B 792 " pdb="ZN ZN B 902 " model vdw 1.973 2.230 nonbonded pdb=" OD2 ASP B 792 " pdb="ZN ZN B 902 " model vdw 2.034 2.230 nonbonded pdb=" OG SER B 793 " pdb="ZN ZN B 902 " model vdw 2.125 2.230 nonbonded pdb=" OH TYR B 321 " pdb=" O SER B 387 " model vdw 2.170 3.040 nonbonded pdb=" CG ASP B 792 " pdb="ZN ZN B 902 " model vdw 2.197 2.460 ... (remaining 133123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.790 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16475 Z= 0.304 Angle : 0.753 7.058 22609 Z= 0.513 Chirality : 0.052 0.394 2508 Planarity : 0.010 0.137 2640 Dihedral : 16.633 161.096 6329 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 1790 helix: -0.88 (0.19), residues: 525 sheet: 0.25 (0.24), residues: 440 loop : -0.46 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.004 ARG B 796 TYR 0.025 0.005 TYR B 439 PHE 0.018 0.002 PHE C 700 TRP 0.030 0.002 TRP C 402 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.30 (16468) covalent geometry : angle 0.75228 / 0.51 (22606) hydrogen bonds : bond 0.16621 / 10.88 ( 687) hydrogen bonds : angle 7.12145 / 4.87 ( 1889) metal coordination : bond 0.01337 / 0.60 ( 7) metal coordination : angle 2.69155 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6451 (ttp80) cc_final: 0.5908 (mmm160) REVERT: A 255 TYR cc_start: 0.8215 (m-10) cc_final: 0.7937 (m-10) REVERT: A 627 ASN cc_start: 0.9149 (m110) cc_final: 0.8942 (m110) REVERT: A 708 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9237 (mm-30) REVERT: B 681 MET cc_start: 0.8762 (tpt) cc_final: 0.8481 (tpt) REVERT: B 710 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7875 (ptp-170) REVERT: B 733 HIS cc_start: 0.8948 (m170) cc_final: 0.8712 (m-70) REVERT: C 683 LEU cc_start: 0.8636 (mp) cc_final: 0.8145 (tp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1601 time to fit residues: 43.5811 Evaluate side-chains 121 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0030 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS A 272 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN C 687 HIS C 807 HIS C 857 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098305 restraints weight = 24961.564| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.45 r_work: 0.3052 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16475 Z= 0.149 Angle : 0.661 8.084 22609 Z= 0.361 Chirality : 0.046 0.353 2508 Planarity : 0.005 0.089 2640 Dihedral : 18.549 159.377 2733 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.94 % Allowed : 3.38 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 1790 helix: 0.74 (0.22), residues: 535 sheet: 0.37 (0.24), residues: 427 loop : 0.14 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 309 TYR 0.029 0.002 TYR A 296 PHE 0.015 0.002 PHE C 391 TRP 0.020 0.001 TRP B 805 HIS 0.008 0.001 HIS A 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (16468) covalent geometry : angle 0.66036 / 0.36 (22606) hydrogen bonds : bond 0.04890 / 3.15 ( 687) hydrogen bonds : angle 5.13682 / 3.56 ( 1889) metal coordination : bond 0.00470 / 0.30 ( 7) metal coordination : angle 1.41837 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6586 (ttp80) cc_final: 0.6075 (mmm160) REVERT: A 238 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8242 (t-90) REVERT: A 296 TYR cc_start: 0.7648 (m-80) cc_final: 0.7124 (m-80) REVERT: A 329 MET cc_start: 0.8888 (tpp) cc_final: 0.7929 (tpp) REVERT: A 444 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8298 (mt0) REVERT: A 623 GLU cc_start: 0.8838 (tt0) cc_final: 0.8512 (tt0) REVERT: A 627 ASN cc_start: 0.9135 (m110) cc_final: 0.8921 (m110) REVERT: A 669 GLU cc_start: 0.8520 (tp30) cc_final: 0.7990 (tm-30) REVERT: A 686 LYS cc_start: 0.8968 (tptp) cc_final: 0.8418 (tptp) REVERT: B 681 MET cc_start: 0.8849 (tpt) cc_final: 0.8614 (tpt) REVERT: B 710 ARG cc_start: 0.8631 (ttm110) cc_final: 0.8253 (ptp-170) REVERT: C 683 LEU cc_start: 0.8738 (mp) cc_final: 0.8172 (tp) REVERT: C 811 ARG cc_start: 0.8786 (mtm180) cc_final: 0.8456 (ttp-110) outliers start: 15 outliers final: 8 residues processed: 142 average time/residue: 0.1526 time to fit residues: 31.4062 Evaluate side-chains 128 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 87 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 149 optimal weight: 0.0970 chunk 125 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 156 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 113 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.139570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.097369 restraints weight = 25265.239| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.57 r_work: 0.3056 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16475 Z= 0.137 Angle : 0.601 6.703 22609 Z= 0.329 Chirality : 0.045 0.335 2508 Planarity : 0.004 0.065 2640 Dihedral : 18.544 159.402 2733 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.75 % Allowed : 4.82 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1790 helix: 1.18 (0.23), residues: 530 sheet: 0.25 (0.24), residues: 427 loop : 0.27 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 728 TYR 0.023 0.001 TYR A 296 PHE 0.049 0.002 PHE A 290 TRP 0.012 0.001 TRP C 402 HIS 0.013 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (16468) covalent geometry : angle 0.60102 / 0.33 (22606) hydrogen bonds : bond 0.04533 / 2.91 ( 687) hydrogen bonds : angle 4.79712 / 3.34 ( 1889) metal coordination : bond 0.00413 / 0.22 ( 7) metal coordination : angle 1.74607 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6531 (ttp80) cc_final: 0.6033 (mmm160) REVERT: A 238 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.8118 (t-90) REVERT: A 296 TYR cc_start: 0.7647 (m-80) cc_final: 0.7440 (m-80) REVERT: A 329 MET cc_start: 0.9008 (tpp) cc_final: 0.8579 (tpp) REVERT: A 444 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8302 (mt0) REVERT: A 623 GLU cc_start: 0.8798 (tt0) cc_final: 0.8477 (tt0) REVERT: A 627 ASN cc_start: 0.9130 (m110) cc_final: 0.8929 (m110) REVERT: A 669 GLU cc_start: 0.8534 (tp30) cc_final: 0.8033 (tm-30) REVERT: A 686 LYS cc_start: 0.8932 (tptp) cc_final: 0.8659 (tptp) REVERT: B 681 MET cc_start: 0.8795 (tpt) cc_final: 0.8542 (tpt) REVERT: C 683 LEU cc_start: 0.8734 (mp) cc_final: 0.8177 (tp) REVERT: C 811 ARG cc_start: 0.8762 (mtm180) cc_final: 0.8504 (ttp-110) outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 0.1461 time to fit residues: 26.1119 Evaluate side-chains 119 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091918 restraints weight = 24725.254| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.11 r_work: 0.2912 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16475 Z= 0.187 Angle : 0.617 7.300 22609 Z= 0.333 Chirality : 0.046 0.318 2508 Planarity : 0.004 0.059 2640 Dihedral : 18.668 158.093 2733 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.06 % Allowed : 5.88 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1790 helix: 1.34 (0.23), residues: 527 sheet: 0.05 (0.24), residues: 434 loop : 0.15 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 759 TYR 0.018 0.002 TYR A 296 PHE 0.019 0.002 PHE A 290 TRP 0.018 0.001 TRP B 805 HIS 0.015 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (16468) covalent geometry : angle 0.61641 / 0.33 (22606) hydrogen bonds : bond 0.04391 / 2.80 ( 687) hydrogen bonds : angle 4.60312 / 3.21 ( 1889) metal coordination : bond 0.00826 / 0.43 ( 7) metal coordination : angle 2.47197 / 1.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.6534 (ttp80) cc_final: 0.6252 (mmm160) REVERT: A 238 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.8226 (t-90) REVERT: A 255 TYR cc_start: 0.8264 (m-10) cc_final: 0.8050 (m-10) REVERT: A 296 TYR cc_start: 0.7661 (m-80) cc_final: 0.7284 (m-80) REVERT: A 329 MET cc_start: 0.8836 (tpp) cc_final: 0.8450 (tpp) REVERT: A 623 GLU cc_start: 0.8727 (tt0) cc_final: 0.8443 (tt0) REVERT: B 725 ARG cc_start: 0.8566 (mmm160) cc_final: 0.8108 (mmm160) REVERT: C 683 LEU cc_start: 0.8716 (mp) cc_final: 0.8203 (tp) REVERT: C 811 ARG cc_start: 0.8742 (mtm180) cc_final: 0.8520 (ttp-110) REVERT: C 866 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8190 (t) outliers start: 17 outliers final: 10 residues processed: 130 average time/residue: 0.1464 time to fit residues: 27.8183 Evaluate side-chains 123 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 102 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 31 optimal weight: 40.0000 chunk 145 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 135 optimal weight: 0.0060 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.0050 chunk 85 optimal weight: 2.9990 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN A 627 ASN C 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.092688 restraints weight = 24906.058| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.09 r_work: 0.2937 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16475 Z= 0.135 Angle : 0.577 9.306 22609 Z= 0.312 Chirality : 0.044 0.318 2508 Planarity : 0.004 0.044 2640 Dihedral : 18.639 157.615 2733 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.06 % Allowed : 7.19 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1790 helix: 1.53 (0.23), residues: 528 sheet: 0.06 (0.24), residues: 425 loop : 0.14 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 728 TYR 0.013 0.001 TYR A 294 PHE 0.029 0.001 PHE A 290 TRP 0.015 0.001 TRP B 805 HIS 0.014 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16468) covalent geometry : angle 0.57638 / 0.31 (22606) hydrogen bonds : bond 0.04083 / 2.60 ( 687) hydrogen bonds : angle 4.48156 / 3.12 ( 1889) metal coordination : bond 0.00565 / 0.29 ( 7) metal coordination : angle 2.30216 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.8216 (t-90) REVERT: A 255 TYR cc_start: 0.8241 (m-10) cc_final: 0.7980 (m-10) REVERT: A 296 TYR cc_start: 0.7594 (m-80) cc_final: 0.7251 (m-80) REVERT: A 623 GLU cc_start: 0.8720 (tt0) cc_final: 0.8460 (tt0) REVERT: C 683 LEU cc_start: 0.8715 (mp) cc_final: 0.8203 (tp) REVERT: C 811 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8496 (ttp-110) REVERT: C 866 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8155 (t) outliers start: 17 outliers final: 11 residues processed: 131 average time/residue: 0.1329 time to fit residues: 26.2330 Evaluate side-chains 125 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 133 optimal weight: 0.1980 chunk 161 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 128 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN A 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093352 restraints weight = 24870.135| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.05 r_work: 0.2953 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16475 Z= 0.128 Angle : 0.571 10.767 22609 Z= 0.304 Chirality : 0.043 0.313 2508 Planarity : 0.004 0.044 2640 Dihedral : 18.648 157.181 2733 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.38 % Allowed : 7.44 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1790 helix: 1.69 (0.23), residues: 529 sheet: 0.05 (0.24), residues: 432 loop : 0.14 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.013 0.001 TYR A 296 PHE 0.035 0.001 PHE A 290 TRP 0.015 0.001 TRP B 805 HIS 0.015 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (16468) covalent geometry : angle 0.57084 / 0.30 (22606) hydrogen bonds : bond 0.03925 / 2.50 ( 687) hydrogen bonds : angle 4.35184 / 3.05 ( 1889) metal coordination : bond 0.00451 / 0.23 ( 7) metal coordination : angle 2.11439 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.8190 (t-90) REVERT: A 296 TYR cc_start: 0.7542 (m-10) cc_final: 0.7222 (m-80) REVERT: A 329 MET cc_start: 0.8287 (tpp) cc_final: 0.7867 (tpp) REVERT: A 623 GLU cc_start: 0.8717 (tt0) cc_final: 0.8465 (tt0) REVERT: A 669 GLU cc_start: 0.8445 (tp30) cc_final: 0.8011 (tm-30) REVERT: A 686 LYS cc_start: 0.8964 (tppt) cc_final: 0.8553 (tptp) REVERT: B 441 CYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8219 (t) REVERT: C 811 ARG cc_start: 0.8744 (mtm180) cc_final: 0.8430 (ttp-110) REVERT: C 866 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8074 (t) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 0.1472 time to fit residues: 30.0516 Evaluate side-chains 132 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 866 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 23 optimal weight: 0.8980 chunk 100 optimal weight: 0.0060 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 0.0670 chunk 169 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.093629 restraints weight = 24961.385| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.06 r_work: 0.2954 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16475 Z= 0.126 Angle : 0.569 10.170 22609 Z= 0.304 Chirality : 0.043 0.311 2508 Planarity : 0.004 0.082 2640 Dihedral : 18.635 156.641 2733 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.13 % Allowed : 8.19 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1790 helix: 1.65 (0.23), residues: 535 sheet: 0.07 (0.24), residues: 430 loop : 0.15 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 728 TYR 0.017 0.001 TYR A 294 PHE 0.023 0.001 PHE A 290 TRP 0.015 0.001 TRP B 805 HIS 0.021 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (16468) covalent geometry : angle 0.56825 / 0.30 (22606) hydrogen bonds : bond 0.03798 / 2.42 ( 687) hydrogen bonds : angle 4.28724 / 3.01 ( 1889) metal coordination : bond 0.00402 / 0.21 ( 7) metal coordination : angle 1.95161 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8231 (t-90) REVERT: A 239 SER cc_start: 0.7884 (m) cc_final: 0.7498 (p) REVERT: A 296 TYR cc_start: 0.7456 (m-10) cc_final: 0.7225 (m-80) REVERT: A 623 GLU cc_start: 0.8690 (tt0) cc_final: 0.8461 (tt0) REVERT: A 669 GLU cc_start: 0.8435 (tp30) cc_final: 0.8040 (tm-30) REVERT: A 686 LYS cc_start: 0.8891 (tppt) cc_final: 0.8526 (tptp) REVERT: B 441 CYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8280 (t) REVERT: C 811 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8413 (ttp-110) outliers start: 18 outliers final: 13 residues processed: 133 average time/residue: 0.1278 time to fit residues: 25.8035 Evaluate side-chains 133 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 179 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 368 GLN ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096132 restraints weight = 25119.189| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.30 r_work: 0.3006 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16475 Z= 0.169 Angle : 0.598 9.594 22609 Z= 0.315 Chirality : 0.044 0.309 2508 Planarity : 0.004 0.047 2640 Dihedral : 18.658 155.905 2733 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.44 % Allowed : 8.63 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1790 helix: 1.60 (0.22), residues: 539 sheet: 0.02 (0.24), residues: 438 loop : 0.15 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 215 TYR 0.011 0.001 TYR C 461 PHE 0.025 0.002 PHE A 290 TRP 0.014 0.001 TRP B 805 HIS 0.016 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (16468) covalent geometry : angle 0.59712 / 0.32 (22606) hydrogen bonds : bond 0.03951 / 2.52 ( 687) hydrogen bonds : angle 4.30908 / 3.02 ( 1889) metal coordination : bond 0.00673 / 0.34 ( 7) metal coordination : angle 2.19311 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.8327 (t-90) REVERT: A 239 SER cc_start: 0.7819 (m) cc_final: 0.7348 (p) REVERT: A 329 MET cc_start: 0.8264 (tpp) cc_final: 0.7802 (tpp) REVERT: A 623 GLU cc_start: 0.8726 (tt0) cc_final: 0.8455 (tt0) REVERT: A 631 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8390 (tt) REVERT: A 669 GLU cc_start: 0.8507 (tp30) cc_final: 0.8103 (tm-30) REVERT: A 686 LYS cc_start: 0.8945 (tppt) cc_final: 0.8588 (tptp) REVERT: B 441 CYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8250 (t) REVERT: C 811 ARG cc_start: 0.8587 (mtm180) cc_final: 0.8266 (ttp-110) outliers start: 23 outliers final: 17 residues processed: 141 average time/residue: 0.1269 time to fit residues: 27.2908 Evaluate side-chains 139 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 40.0000 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 175 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 123 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.138250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096781 restraints weight = 24876.754| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.33 r_work: 0.3027 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16475 Z= 0.133 Angle : 0.569 7.884 22609 Z= 0.304 Chirality : 0.043 0.310 2508 Planarity : 0.004 0.049 2640 Dihedral : 18.635 155.779 2733 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.25 % Allowed : 9.51 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1790 helix: 1.65 (0.22), residues: 539 sheet: 0.02 (0.24), residues: 438 loop : 0.13 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 215 TYR 0.046 0.001 TYR A 296 PHE 0.015 0.001 PHE A 635 TRP 0.015 0.001 TRP B 805 HIS 0.016 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16468) covalent geometry : angle 0.56842 / 0.30 (22606) hydrogen bonds : bond 0.03751 / 2.39 ( 687) hydrogen bonds : angle 4.30133 / 3.02 ( 1889) metal coordination : bond 0.00473 / 0.24 ( 7) metal coordination : angle 2.01938 / 1.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.8337 (t-90) REVERT: A 239 SER cc_start: 0.7922 (m) cc_final: 0.7453 (p) REVERT: A 329 MET cc_start: 0.8375 (tpp) cc_final: 0.7931 (tpp) REVERT: A 623 GLU cc_start: 0.8772 (tt0) cc_final: 0.8537 (tt0) REVERT: A 631 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8377 (tt) REVERT: A 669 GLU cc_start: 0.8536 (tp30) cc_final: 0.8120 (tm-30) REVERT: A 686 LYS cc_start: 0.8911 (tppt) cc_final: 0.8553 (tptp) REVERT: B 441 CYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8375 (t) REVERT: B 733 HIS cc_start: 0.8980 (m170) cc_final: 0.8717 (m90) REVERT: C 469 CYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8134 (m) REVERT: C 811 ARG cc_start: 0.8748 (mtm180) cc_final: 0.8395 (ttp-110) REVERT: C 818 MET cc_start: 0.8149 (ttp) cc_final: 0.7806 (ttp) outliers start: 20 outliers final: 13 residues processed: 131 average time/residue: 0.1322 time to fit residues: 26.3345 Evaluate side-chains 133 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 143 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.138585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096996 restraints weight = 24960.202| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.42 r_work: 0.3036 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16475 Z= 0.135 Angle : 0.570 7.701 22609 Z= 0.304 Chirality : 0.043 0.310 2508 Planarity : 0.004 0.050 2640 Dihedral : 18.630 155.507 2733 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.19 % Allowed : 9.38 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1790 helix: 1.73 (0.22), residues: 539 sheet: -0.03 (0.24), residues: 445 loop : 0.10 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 215 TYR 0.042 0.001 TYR A 296 PHE 0.015 0.001 PHE A 635 TRP 0.016 0.001 TRP B 805 HIS 0.015 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16468) covalent geometry : angle 0.57007 / 0.30 (22606) hydrogen bonds : bond 0.03713 / 2.38 ( 687) hydrogen bonds : angle 4.26739 / 3.00 ( 1889) metal coordination : bond 0.00456 / 0.23 ( 7) metal coordination : angle 1.98349 / 1.00 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.8396 (t-90) REVERT: A 239 SER cc_start: 0.7879 (m) cc_final: 0.7407 (p) REVERT: A 329 MET cc_start: 0.8468 (tpp) cc_final: 0.8039 (tpp) REVERT: A 623 GLU cc_start: 0.8806 (tt0) cc_final: 0.8578 (tt0) REVERT: A 631 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 669 GLU cc_start: 0.8555 (tp30) cc_final: 0.8073 (tm-30) REVERT: A 686 LYS cc_start: 0.8887 (tppt) cc_final: 0.8523 (tptp) REVERT: B 441 CYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8378 (t) REVERT: B 733 HIS cc_start: 0.9000 (m170) cc_final: 0.8761 (m90) REVERT: C 469 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8132 (m) REVERT: C 811 ARG cc_start: 0.8770 (mtm180) cc_final: 0.8406 (ttp-110) outliers start: 19 outliers final: 14 residues processed: 134 average time/residue: 0.1320 time to fit residues: 27.0093 Evaluate side-chains 136 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 469 CYS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 707 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 99 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 124 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 170 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.138197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095702 restraints weight = 24900.623| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.27 r_work: 0.3022 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16475 Z= 0.142 Angle : 0.578 7.192 22609 Z= 0.308 Chirality : 0.043 0.310 2508 Planarity : 0.004 0.050 2640 Dihedral : 18.632 155.123 2733 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.31 % Allowed : 9.44 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1790 helix: 1.76 (0.22), residues: 539 sheet: -0.05 (0.24), residues: 445 loop : 0.05 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 215 TYR 0.052 0.002 TYR A 296 PHE 0.016 0.001 PHE A 635 TRP 0.016 0.001 TRP B 805 HIS 0.012 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16468) covalent geometry : angle 0.57794 / 0.31 (22606) hydrogen bonds : bond 0.03722 / 2.38 ( 687) hydrogen bonds : angle 4.26219 / 2.99 ( 1889) metal coordination : bond 0.00464 / 0.23 ( 7) metal coordination : angle 2.00694 / 1.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4053.20 seconds wall clock time: 70 minutes 13.34 seconds (4213.34 seconds total)